I would load the bike the way you ride it with saddlebag, bottles, other attachments, lift it 6" off the ground and drop it, listen and try an figure out where the noise is coming from. Possible places I can think of are headset, cables close to each other in the handlebar area, cables entering/exiting frame, cables inside the frame, plastic cable guide under the bb, saddle rails to saddle interface, loose spoke, inner tube valve loose around the rim.